Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate 209326 DVU0390 glycolate oxidase, subunit GlcD, putative
Query= BRENDA::H6LBS1 (466 letters) >MicrobesOnline__882:209326 Length = 460 Score = 263 bits (672), Expect = 9e-75 Identities = 152/456 (33%), Positives = 233/456 (51%), Gaps = 14/456 (3%) Query: 17 LIPAERVFVGTEIGEDFSHDELGS--------IHSYPEVLIKVTSTEEVSKIMKYAYEHN 68 L PA R + +G D D G+ + + P++++ S ++ +M+ A EH Sbjct: 8 LTPALRTAIIDAVGRDAVLDTAGAPYDRDASELRATPDMVVLPESVGQIQALMRLATEHR 67 Query: 69 IPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEE 128 PV+ RG GTGL G C+ L GG++L MN + +DT NL V+ G + L Sbjct: 68 FPVIPRGGGTGLAGGCLALMGGVVLSVERMNRVRAIDTRNLVAEVDAGCITQTLRDAAAA 127 Query: 129 NDLFYPPDP-GEKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIV 187 +LFYPPDP G +T+ GN++TNAGG VKYGVTRDYV G+ VL +GE++ G + Sbjct: 128 ANLFYPPDPAGMDRSTVGGNVATNAGGPACVKYGVTRDYVLGVEAVLPDGELLRAGVRTR 187 Query: 188 KNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSK 247 K GY + L+ GSEGTL VIT +KL+PLP T+ + + F ++ A V ++ + Sbjct: 188 KGVVGYDMAHLLCGSEGTLGVITGLTMKLIPLPAATVGMAVAFADMPSAMRAVAAVLGAG 247 Query: 248 AIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAE 307 +P+AIEFM+ + + + L FP + +L+ + +E + + VA +C + Sbjct: 248 HLPSAIEFMDHRCLALVGEML--PFPVPGARPSLLIIELDGQRATIEPQLDAVAAICREQ 305 Query: 308 GAKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLAKE 367 GA V T + ++W R I DV VP IA+ + + Sbjct: 306 GATQVLPAPTDAERATIWGVRRQVSLRIHDYAGLYLSEDVAVPLVAIADLVAELPAFEER 365 Query: 368 MDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEHGIGY 427 + I +FGHAGDGN+H+ V D + E + + + + G +SGEHGIG Sbjct: 366 YGLEIFAFGHAGDGNIHLNVTSS---STDNRERAEEGVVALARRVVELGGTISGEHGIGE 422 Query: 428 AKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 AK+ + + +AL GI+ FDP ++NP KV Sbjct: 423 AKKHLVPLELSARSIALQKGIRGVFDPLGIMNPGKV 458 Lambda K H 0.318 0.136 0.388 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 489 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 466 Length of database: 460 Length adjustment: 33 Effective length of query: 433 Effective length of database: 427 Effective search space: 184891 Effective search space used: 184891 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory